Microbiology: Binomial Nomenclature and Microbes

• Microbiology Exam 1 Study Notes

Binomial Nomenclature

• Identifies organisms by genus and species.
• Written as Genus species (Genus capitalized, species not capitalized).
• Can be shortened to G. species after the first use.
• Should be underlined or italicized.
• Established by Carolus Linnaeus.

Characteristics of Microbes

• Bacteria: Prokaryotic, single-celled, peptidoglycan walls, divides by binary fission, nutrition from organic/inorganic chemicals or photosynthesis, motile by flagella.
• Fungi: Eukaryotic, chitin cell walls, nutrition from organic chemicals. Yeasts are unicellular; molds and mushrooms are multicellular.
• Molds: Consist of masses of mycelia, which are composed of filaments called hyphae
• Algae: Eukaryotic, cellulose cell walls, found in soil, freshwater, and saltwater, nutrition via photosynthesis, reproduces sexually or asexually.
• Protozoa: Eukaryotic, nutrition from organic chemicals, move using flagella, pseudopods, or cilia, free-living or parasitic, some are photosynthetic, reproduce sexually or asexually, unicellular (AKA helminth).
• Viruses: Acellular, DNA or RNA core surrounded by a protein coat (lipid envelope may be present), replicates only within a living host cell.

Concepts in Microbiology

• Biogenesis: Living cells arise only from preexisting living cells.
• Spontaneous Generation: Life arises from nonliving matter, requiring a "vital force," disproved by Francesco Redi.

Key Figures in Microbiology History

• Robert Hooke: Reported that living things are made of cells, initiating cell theory.
• Antonie van Leeuwenhoek: Discovered protists and bacteria, called microscopic organisms "animalcules."
• Francesco Redi: Experimented with decaying meat in jars to disprove spontaneous generation.
• John Needham: Observed microbial growth in boiled nutrient broth in covered flasks.
• Lazzaro Spallanzani: Observed no microbial growth in boiled nutrient solutions in sealed flasks.
• Rudolf Virchow: Proposed that new cells are formed only from existing cells.
• Louis Pasteur: Demonstrated microorganisms are in the air using S-shaped flasks; showed microorganisms responsible for fermentation; disproved spontaneous generation.
• Robert Koch: Discovered that bacterium causes anthrax and established Koch's postulates.
• Ignaz Semmelweis: Advocated handwashing to prevent puerperal fever transmission.
• Joseph Lister: Used chemical antiseptic (phenol) to prevent surgical wound infections.
• Edward Jenner: Discovered the smallpox vaccine through cowpox inoculation.
• Paul Ehrlich: Introduced the concept of a "magic bullet" to destroy pathogens without harming the host.
• Alexander Fleming: Discovered penicillin, an antibiotic made by Penicillium fungus, that kills S. aureus.
• Rebecca Lancefield: Classified streptococci based on cell wall components.
• George Beadle and Edward Tatum: Showed that genes encode a cell's enzymes.
• Oswald Avery, Colin MacLeod, and Maclyn McCarty: Showed that DNA is the hereditary material.
• James Watson and Francis Crick: Proposed a model of DNA structure

Processes in Microbiology

• Pasteurization: Using high heat for a short time to kill harmful bacteria in beverages.
• Koch's Postulates: Used to prove that a specific bacteria is causing a specific disease.
  • Microorganism abundant in diseased organisms, not in healthy organisms.
  • Microorganism isolated and grown in pure culture.
  • Cultured microorganism causes disease when introduced into a healthy organism.
  • Microorganism re-isolated from the diseased organism is the same as the original.
• Gram Staining: Classifies bacteria into gram-positive or gram-negative based on cell wall structure.

Microbial Groups and Study Areas

• Prokaryotes: Include bacteria and archaea.
• Eukaryotes: Include fungi, protozoa, algae, and multicellular animal parasites.
• Ehrlich's "Magic Bullet": To destroy a pathogen without harming the host.
• Bacteriology: Study of bacteria.
• Mycology: Study of fungi.
• Parasitology: Study of parasites and protozoa.
• Virology: Study of viruses.
• Microbial Genetics: Study of how microbes inherit traits.
• Genomics: Study of an organism's genes.
• Molecular Biology: Study of how DNA directs protein synthesis.
• Recombinant DNA: DNA made from two different sources.
• Recombinant Technology: Combines genes from different sources into a single DNA molecule.
• Immunology: Study of the immune system.

Metric Conversions

• 1 mL = 0.001 L
• 1 L = 1,000,000 uL
• 1 mL = 1000 uL
• 1 uL = 10^-6 L
• 1 L = 1000 mL
• 1 uL = 0.001 mL

Microscopy Concepts

• Total Magnification: Calculated by multiplying the objective lens magnification by the ocular lens magnification.
• Resolution: The ability of lenses to distinguish two points; shorter wavelengths of light provide greater resolution.
• Immersion Oil: Used to prevent light refraction.
• Bright-field Microscope: Produces a dark image against a brighter background.
• Dark-field Microscope: Light objects are visible against a dark background; only light reflected off the specimen enters the objective lens.
• Phase Contrast Microscope: Allows examination of living organisms and internal cell structures; brings together direct and diffracted light rays to form an image.
• Differential Interference Contrast Microscope: Uses two light beams and prisms for increased contrast and color.
• Transmission Electron Microscope: Beam of electrons passes through ultrathin sections, magnified 10,000 to 10,000,000x, offers best resolution and magnification, specimens stained with heavy-metal salts..

Staining Procedures

• Acid-Fast Stain: Binds to bacteria with waxy material in cell walls.
  • Primary stain: Carbolfuchsin.
  • Decolorizing agent: Acid-alcohol.
  • Counterstain: Methylene blue.
  • Acid-fast bacteria appear red, non-acid-fast appear blue.
• Endospore Stain: Stains resistant, dormant endospores.
  • Primary stain: Malachite green (with heat).
  • Decolorizer: Water.
  • Counterstain: Safranin.
  • Spores appear green within red/pink cells.
• Gram Stain: Classifies bacteria into gram-positive or gram-negative.
  • Gram-positive: Thick peptidoglycan cell walls, purple.
  • Gram-negative: Thin peptidoglycan cell walls with lipopolysaccharides, pink/red after safranin.
• Negative Stain: Colors the background to make capsules more visible.

Smear Preparation

• Air dry to keep bacteria in place.
• Heat fix to ensure no contamination.
• Light from the condenser passes through the objective lens.

Cell Structure Comparison

• Prokaryotic Cell: Single, circular chromosome (not in a membrane), no histones, no organelles, peptidoglycan or pseudomurein cell walls, divides by binary fission.
• Eukaryotic Cell: Paired chromosomes in nuclear membrane, histones, organelles, polysaccharide cell walls, divides by mitosis.
• Key Difference: Prokaryotes lack a nucleus.

Bacterial Characteristics

• Size: 0.2 to 2.0 μm diameter × 2 to 8 μm length.
• Monomorphic: Single-shaped.
• Pleomorphic: Many shapes.
• Shapes: Coccus, bacillus, spirillum, vibrio, spirochete, star-shaped, rectangular.

Arrangement of Bacterial Cells Observed Microscopically

• Streptococci: Chain-like patterns.
• Bacillus: Rod shaped bacteria.
• Coccus: Spherical bacteria.
• Pairs: Diplococci, diplobacilli.
• Clusters: Staphylococci.
• Chains: Streptococci, streptobacilli.
• Groups of Four: Tetrads.
• Cube-like Groups of Eight: Sarcinae.

Bacterial Structures and Function

• Pili: Hair-like structures for adhesion, important for colonization and infection, involved in movement.
• Capsule: Polysaccharide layer outside the cell envelope, prevents phagocytosis, neatly organized and firmly attached, contributes to bacterial virulence.
• Glycocalyx: Dense, gel-like meshwork surrounding the cell, physical barrier, modulates cell adhesion, made of polysaccharide and/or polypeptide, external to the cell wall.
• Flagella: Filamentous appendages for propulsion, made of flagellin protein.
  • Filament: Outermost region.
  • Hook: Attaches to the filament.
  • Basal Body: Anchors flagellum to the cell wall and membrane.
• Cilia: Small hair-like protuberances for locomotion and sensory functions (eukaryotic cells).
• Fimbriae: Hair-like appendages for attachment; enable the bacteria to bind to specific receptor structures and thereby to colonize specific surfaces

Gram-Positive Cell Wall and Membrane

• Thick peptidoglycan wall.
• Teichoic acids: Contribute to surface charge and hydrophobicity, affecting molecule binding.
• Polysaccharides and teichoic acids provide antigenic specificity.

Gram-Negative Cell Wall and Membrane

• Thin peptidoglycan wall.
• Outer membrane: Protects from phagocytes and antibiotics.
• Periplasmic space: Space between inner and outer membranes containing peptidoglycan.
• Lipopolysaccharide (LPS): Lipid A (endotoxin) embedded in the top layer.
• Porins: Proteins forming channels through the membrane.

Gram Staining Steps and Purpose

• Applying crystal violet (primary stain): Adheres to the cell membranes of both gram negative and positive cells
• Adding Gram's iodine (mordant): Enhances stain affinity by binding to the primary stain.
• Decolorization with ethanol/acetone: Dehydrates peptidoglycan, shrinking and tightening it.
• Counterstaining with safranin: Stains decolorized bacteria; distinguishes gram-negative from gram-positive bacteria.
• Gram-positive appearance: Purple.
• Gram-negative appearance: Red/Pink.

Cell Wall Components

• NAM full name: N-acetylmuramic acid.
• NAG full name: N-acetylglucosamine.

Study notes covering binomial nomenclature and characteristics of microbes. Binomial nomenclature identifies organisms by genus and species, as established by Carolus Linnaeus. Microbes include bacteria, fungi, algae, and protozoa, each with unique characteristics.